A significant proportion of the 23 known human-specific duplicated genes are implicated in neurological processes. The Rho GTPase activating protein 11 (ARHGAP11) is one such gene that is also found in an area associated with schizophrenia, intellectual disability, and autism. We determined that the human-specific duplicated copy (ARHGAP11B) duplicated 5.3 million years ago (mya) shortly after the human-chimpanzee divergence (~ 6.5 mya). The human-specific duplicated copy is not found in all humans, and represents an incomplete version of ARHGAP11A, suggesting a potentially alternative function. The goal of my project was to identify sequence differences between A (ancestral) and B (duplicated) paralogs (i.e., genes related by duplication within the same species) and use these differences to assess gene variation and expression. By sequencing 64 different transcripts (i.e. protein coding regions) we found nine “paralog-specific variants” (or PSVs) allowing us to distinguish between A and B. We assessed the level of gene expression (how much a gene is “used”) for each paralog in human fetal brain samples and found that A was expressed approximately two times more than B. Interestingly, we found similar results from other tissue types including blood. Further, we have used these PSVs to identify potentially pathogenic mutations of ARHGAP11A from targeted large-scale sequencing data of a collection of children with intellectual disability. We are using these data to understand the function of different members of the ARHGAP11 gene family both on neurological development and potentially on the evolution of traits that make us uniquely human.